So, I have a bit of an update -- hopefully this will somewhat help others encountering this error, because it may not be entirely a bug...
1. The issue can be overcome by first and foremost not applying walls to a system previously run without any -- that was my mistake and it makes physical sense. Dynamic equilibration has to be performed with walls and corresponding pbc setting. This, however, does not guarantee anything if the system is e.g. solvated -- that is, if there are atoms expected very close to walls, or beyond them. In addition, if there atoms looking for neighbors across the box (through previously set pbc), that can be catastrophic. See below. 2. After solvating, but before EM, reinsert the system in a box slightly larger in the z-direction. For a box initially 4 nm long in Z in my case, reinserting in a 4.6 nm long box worked here. 3. Particles seem to be lost when wall-r-linpot is set improperly, so try various values (0.25 nm worked for me). 4. The entire concept here is naturally very messy. I could think of optional functionality, which allows for removing entire molecules whose atoms are anticipated to be beyond walls, or close enough to result in local explosions. However, that is also messy and can be done manually in previous steps, so no elegant suggestion from my end, unfortunately, other than being very mindful when setting this up. Alex On Wed, Nov 1, 2017 at 6:26 PM, Alex <nedoma...@gmail.com> wrote: > Mark, > > Could you please share your email address, so I can send you the tpr > privately? I don't want this work to be public just yet, if that's okay. > > Thanks, > > Alex > > > On 11/1/2017 4:42 PM, Mark Abraham wrote: > >> Hi, >> >> We have had several reports of "lost particles while sorting" but we would >> like a .tpr on an issue on redmine.gromacs.org to be able to investigate, >> please! >> >> Mark >> >> On Wed, Nov 1, 2017 at 10:19 PM Alex <nedoma...@gmail.com> wrote: >> >> Hi all, >>> >>> I am using walls in the cowboy mode, GMX v. 2016.3, system is a porous >>> membrane (periodic in XY) with water and ions -- everything works fine >>> with >>> pbc=xyz and no walls. With walls, mdrun throws "Software inconsistency >>> error: Lost particles while sorting." >>> >>> mdp exerpt below: >>> >>> pbc = xy >>> nwall = 2 >>> wall-type = 12-6 >>> wall-r-linpot = 0.0 >>> wall_atomtype = opls_996 opls_996 >>> wall-ewald-zfac = 3 >>> periodic_molecules = yes >>> ns_type = grid >>> rlist = 1.0 >>> coulombtype = pme >>> ewald-geometry = 3dc >>> fourierspacing = 0.135 >>> rcoulomb = 1.0 >>> rvdw = 1.0 >>> vdwtype = cut-off >>> cutoff-scheme = Verlet >>> >>> This uses a custom type "opls_996" properly defined in ffnonbonded of the >>> FF (custom OPLSAA). Any suggestions? I can provide more info, if needed. >>> >>> Thank you, >>> >>> Alex >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.